Fig. 1: Synovial sarcoma is sensitive to disruption of the SUMOylation pathway.

A Each cell type from the DepMap database was analyzed for enrichment in the custom SUMO signature (“SAE1”, “SUMO1”, “SUMO2”, “SUMO3”, “UBA2”, “UBE2I”, “RANBP2”, “CBX4”, “PIAS1”, “PIAS2”, “PIAS3”, “PIAS4”). Cell type-specific genes were ranked by the DEMETER2 v5 dependency scores (“D2_combined_gene_dep_scores.csv” file downloaded 09/18/2019) and analyzed using GSEA (clusterProfiler v.3.14.3 R package [PMID: 22455463]). The enrichment p values were −log10 transformed and used to rank the cells and plot the transformed p values on Y-axis. B RNA levels of genes involved in SUMOylation following shSSX knockdown were obtained from an RNA-seq analysis performed in SS cell lines⁵ C SS cells were transfected with siSSX for 36 h and whole cell lysates were probed with the indicated antibodies. D ChIP-seq enrichment tracks of SS18::SSX in untreated (No Rx = no drug) HS-SY-II cells compared to the tracks of the “input” at the loci of the indicated SUMO components. The combined depth-normalized signal was visualized using IGV browser¹⁰³ and ensuring the same signal range (Y-axis) for each region of interest. E SS cells were treated with increasing concentrations of TAK-981, and cell viability was assessed 72 h later. F HS-SY-II cells underwent CRISPR/Cas9-mediated targeting of the indicated SUMOylation genes and cells were counted and plated at low density and stained with crystal violet 12 days later. G SS cells were transfected with siRNA directed against SSX for 36 h, reseeded, and treated with increasing concentrations of TAK-981 for 72 h before cell viability was assessed; inset is western blotting confirming knockdown. Protein band intensities were quantified like in (C). H SS cells were treated with 100 nM TAK-981 for 36 h or left untreated (No Rx) and whole cell lysates were probed with the indicated antibodies. H shares the same GAPDH blot with Supplementary Fig. 7C. For (E, G) n = 3 biological replicates and data are presented as mean values + SD. Unpaired two-tailed t tests were performed for comparisons between each TAK-981 treatment and No Rx for each cell line in (E) and for comparisons between siControl and siSSX in (G). Exact p values and source data can be found in the Source Data.